OAK RIDGE, Tenn., Jan. 22, 2018 - A team led by the Department of Energy's Oak Ridge National Laboratory has uncovered how certain soil microbes cope in a phosphorus-poor environment to survive in a tropical ecosystem. Their novel approach could be applied in other ecosystems to study various nutrient limitations and inform agriculture and terrestrial biosphere modeling.

Phosphorus is a critical nutrient for global biological processes, such as collecting the sun's energy during photosynthesis and degrading plant debris and soil organic matter. Most tropical ecosystems endure long-term weathering that leaches phosphorus from soil.

The ORNL-led team set out to discover how soil microbial communities respond to the lack of phosphorus and other nutrient deficiencies at the molecular level.

They collected soil samples at the Smithsonian Tropical Research Institute in the Republic of Panama, an experimental field site with phosphorus-rich plots and unfertilized control plots.

"This was the perfect place to test the optimal foraging theory, which is a model that helps predict an organism's behavior when searching for resources," said Chongle Pan, ORNL senior staff scientist and joint associate professor at the University of Tennessee. "We learned how this theory plays out when applied to microbial communities as they compete for nutrients."

The team analyzed the behaviors of many genes and proteins, and in the phosphorus-deficient, untreated soil, they found an increased number of genes responsible for producing phosphorus-acquiring enzymes. They also discovered more than 100 genes that work to pull phosphorus from phytate, which is a complex organic compound found in plant tissue.

"Finding so many genes to break apart and transport such a complex molecule tells us that microbes are hungry for phosphorus in untreated soil," said Melanie Mayes, an ORNL senior staff scientist who studies multi-scale environmental processes.

Conversely, she noted that when phosphorus was plentiful, more genes needed to acquire complex carbon compounds were present. "The microbial community prioritizes the breakdown of the most needed nutrients, focusing efforts on the most limiting element to balance their overall nutritional needs," she said.

The team ran each soil sample through a series of rigorous and comprehensive analyses. The DOE Joint Genome Institute conducted deep sequencing of the soils' metagenomes, or genetic material recovered directly from the soil. ORNL then used mass spectrometry and metaproteomics to identify more than 7,000 proteins in each sample.

These unique tools working together enabled one of the deepest proteogenomics studies done on soil microbial communities, according to Pan.

The ORNL-led team plans to continue their research to characterize the ecology and evolution of soil microbial communities in nutrient-poor environments, which has applications in agriculture and terrestrial biosphere modeling worldwide. Additionally, Mayes and her team are incorporating metagenomics information into nutrient cycling models under a DOE Early Career Research Program Award.

The research was supported by the Laboratory Directed Research and Development program at ORNL. Metagenomic sequencing was conducted by the DOE Joint Genome Institute and soil organic matter analyses were performed using Fourier-transform ion cyclotron resonance mass spectrometry by PNNL's Environmental Molecular Sciences Laboratory, both DOE Office of Science User Facilities. This work also leveraged the Oak Ridge Leadership Computing Facility, a DOE Office of Science User Facility.

ORNL is managed by UT-Battelle for DOE's Office of Science. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit http://science.energy.gov/.

Rye is healthy, thanks to an interplay of microbesEating rye comes with a variety of health benefits. A new study from the University of Eastern Finland now shows that both lactic acid bacteria and gut bacteria contribute to the health benefits of rye.

Microbes help make the coffeeWhen it comes to processing coffee beans, longer fermentation times can result in better taste, contrary to conventional wisdom.

Space microbes aren't so alien after allA new Northwestern University study has found that -- despite its seemingly harsh conditions -- the ISS is not causing bacteria to mutate into dangerous, antibiotic-resistant superbugs.

Trending Science News

Top Science Podcasts

Clint SmithThe killing of George Floyd by a police officer has sparked massive protests nationwide. This hour, writer and scholar Clint Smith reflects on this moment, through conversation, letters, and poetry.

#562 Superbug to BedsideBy now we're all good and scared about antibiotic resistance, one of the many things coming to get us all. But there's good news, sort of. News antibiotics are coming out! How do they get tested? What does that kind of a trial look like and how does it happen? Host Bethany Brookeshire talks with Matt McCarthy, author of "Superbugs: The Race to Stop an Epidemic", about the ins and outs of testing a new antibiotic in the hospital.

GrahamIf former Minneapolis police officer Derek Chauvin's case for the death of George Floyd goes to trial, there will be this one, controversial legal principle looming over the proceedings: The reasonable officer.
In this episode, we explore the origin of the reasonable officer standard, with the case that sent two Charlotte lawyers on a quest for true objectivity, and changed the face of policing in the US.
This episode was produced by Matt Kielty with help from Kelly Prime and Annie McEwen.
Support Radiolab today at Radiolab.org/donate.